comparison fastq_dump.xml @ 13:c38286ea7047 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 686710a7d313b828f1daed20c4055479727f2d91

12:5534eb46de20

    <macros>
        <import>sra_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <version_command>fastq-dump --version</version_command>
    <command detect_errors="exit_code">
        <![CDATA[

    #if $input.input_select=="file_list":
    
        for acc in `cat $input.file_list` ;
        do
    
    #elif $input.input_select=="accession_number":

        ## Stripping leading and trailing spaces in case user typed them in 
        acc="${input.accession}" &&
    
    #end if

    #if $input.input_select=="file_list" or $input.input_select=="accession_number":
    
        [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (
    
    #end if

    ## Need to set the home directory to the current working directory,
    ## else the tool tries to write to home/.ncbi and fails when used
    ## with a cluster manager.
    export HOME=\$PWD &&

13:c38286ea7047

    <macros>
        <import>sra_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <version_command>fastq-dump --version</version_command>
    <command detect_errors="exit_code"><![CDATA[

    @SET_ACCESSIONS@

    ## Need to set the home directory to the current working directory,
    ## else the tool tries to write to home/.ncbi and fails when used
    ## with a cluster manager.
    export HOME=\$PWD &&